/*
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 *    AbstractTimeSeries.java
 *    Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.filters.unsupervised.attribute;

import java.util.Enumeration;
import java.util.Vector;

import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Queue;
import weka.core.Range;
import weka.core.Utils;
import weka.core.WeightedAttributesHandler;
import weka.core.WeightedInstancesHandler;
import weka.filters.Filter;
import weka.filters.UnsupervisedFilter;

/**
 * An abstract instance filter that assumes instances form time-series data and
 * performs some merging of attribute values in the current instance with
 * attribute attribute values of some previous (or future) instance. For
 * instances where the desired value is unknown either the instance may be
 * dropped, or missing values used.
 * <p>
 * 
 * Valid filter-specific options are:
 * <p>
 * 
 * -R index1,index2-index4,...<br>
 * Specify list of columns to calculate new values for. First and last are valid
 * indexes. (default none)
 * <p>
 * 
 * -V <br>
 * Invert matching sense (i.e. calculate for all non-specified columns)
 * <p>
 * 
 * -I num <br>
 * The number of instances forward to merge values between. A negative number
 * indicates taking values from a past instance. (default -1)
 * <p>
 * 
 * -M <br>
 * For instances at the beginning or end of the dataset where the translated
 * values are not known, remove those instances (default is to use missing
 * values).
 * <p>
 * 
 * @author Len Trigg (trigg@cs.waikato.ac.nz)
 * @version $Revision$
 */
public abstract class AbstractTimeSeries extends Filter implements UnsupervisedFilter, OptionHandler, WeightedAttributesHandler, WeightedInstancesHandler {

    /** for serialization */
    private static final long serialVersionUID = -3795656792078022357L;

    /** Stores which columns to copy */
    protected Range m_SelectedCols = new Range();

    /**
     * True if missing values should be used rather than removing instances where
     * the translated value is not known (due to border effects).
     */
    protected boolean m_FillWithMissing = true;

    /**
     * The number of instances forward to translate values between. A negative
     * number indicates taking values from a past instance.
     */
    protected int m_InstanceRange = -1;

    /** Stores the historical instances to copy values between */
    protected Queue m_History;

    /**
     * Returns an enumeration describing the available options.
     * 
     * @return an enumeration of all the available options.
     */
    @Override
    public Enumeration<Option> listOptions() {

        Vector<Option> newVector = new Vector<Option>(4);

        newVector.addElement(new Option("\tSpecify list of columns to translate in time. First and\n" + "\tlast are valid indexes. (default none)", "R", 1, "-R <index1,index2-index4,...>"));
        newVector.addElement(new Option("\tInvert matching sense (i.e. calculate for all non-specified columns)", "V", 0, "-V"));
        newVector.addElement(new Option("\tThe number of instances forward to translate values\n" + "\tbetween. A negative number indicates taking values from\n" + "\ta past instance. (default -1)", "I", 1, "-I <num>"));
        newVector.addElement(new Option("\tFor instances at the beginning or end of the dataset where\n" + "\tthe translated values are not known, remove those instances\n" + "\t(default is to use missing values).", "M", 0, "-M"));

        return newVector.elements();
    }

    /**
     * Parses a given list of options controlling the behaviour of this object.
     * Valid options are:
     * <p>
     * 
     * -R index1,index2-index4,...<br>
     * Specify list of columns to copy. First and last are valid indexes. (default
     * none)
     * <p>
     * 
     * -V<br>
     * Invert matching sense (i.e. calculate for all non-specified columns)
     * <p>
     * 
     * -I num <br>
     * The number of instances forward to translate values between. A negative
     * number indicates taking values from a past instance. (default -1)
     * <p>
     * 
     * -M <br>
     * For instances at the beginning or end of the dataset where the translated
     * values are not known, remove those instances (default is to use missing
     * values).
     * <p>
     * 
     * @param options the list of options as an array of strings
     * @throws Exception if an option is not supported
     */
    @Override
    public void setOptions(String[] options) throws Exception {

        String copyList = Utils.getOption('R', options);
        if (copyList.length() != 0) {
            setAttributeIndices(copyList);
        } else {
            setAttributeIndices("");
        }

        setInvertSelection(Utils.getFlag('V', options));

        setFillWithMissing(!Utils.getFlag('M', options));

        String instanceRange = Utils.getOption('I', options);
        if (instanceRange.length() != 0) {
            setInstanceRange(Integer.parseInt(instanceRange));
        } else {
            setInstanceRange(-1);
        }

        if (getInputFormat() != null) {
            setInputFormat(getInputFormat());
        }

        Utils.checkForRemainingOptions(options);
    }

    /**
     * Gets the current settings of the filter.
     * 
     * @return an array of strings suitable for passing to setOptions
     */
    @Override
    public String[] getOptions() {

        Vector<String> options = new Vector<String>();

        if (!getAttributeIndices().equals("")) {
            options.add("-R");
            options.add(getAttributeIndices());
        }
        if (getInvertSelection()) {
            options.add("-V");
        }
        options.add("-I");
        options.add("" + getInstanceRange());
        if (!getFillWithMissing()) {
            options.add("-M");
        }

        return options.toArray(new String[0]);
    }

    /**
     * Sets the format of the input instances.
     * 
     * @param instanceInfo an Instances object containing the input instance
     *                     structure (any instances contained in the object are
     *                     ignored - only the structure is required).
     * @return true if the outputFormat may be collected immediately
     * @throws Exception if the format couldn't be set successfully
     */
    @Override
    public boolean setInputFormat(Instances instanceInfo) throws Exception {

        super.setInputFormat(instanceInfo);
        resetHistory();
        m_SelectedCols.setUpper(instanceInfo.numAttributes() - 1);
        return false;
    }

    /**
     * Input an instance for filtering. Ordinarily the instance is processed and
     * made available for output immediately. Some filters require all instances be
     * read before producing output.
     * 
     * @param instance the input instance
     * @return true if the filtered instance may now be collected with output().
     * @throws Exception if the input instance was not of the correct format or if
     *                   there was a problem with the filtering.
     */
    @Override
    public boolean input(Instance instance) throws Exception {

        if (getInputFormat() == null) {
            throw new NullPointerException("No input instance format defined");
        }
        if (m_NewBatch) {
            resetQueue();
            m_NewBatch = false;
            resetHistory();
        }

        Instance newInstance = historyInput(instance);
        if (newInstance != null) {
            push(newInstance);
            return true;
        } else {
            return false;
        }
    }

    /**
     * Signifies that this batch of input to the filter is finished. If the filter
     * requires all instances prior to filtering, output() may now be called to
     * retrieve the filtered instances.
     * 
     * @return true if there are instances pending output
     * @throws IllegalStateException if no input structure has been defined
     */
    @Override
    public boolean batchFinished() {

        if (getInputFormat() == null) {
            throw new IllegalStateException("No input instance format defined");
        }
        if (getFillWithMissing() && (m_InstanceRange > 0)) {
            while (!m_History.empty()) {
                push(mergeInstances(null, (Instance) m_History.pop()));
            }
        }
        flushInput();
        m_NewBatch = true;
        m_FirstBatchDone = true;
        return (numPendingOutput() != 0);
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String fillWithMissingTipText() {
        return "For instances at the beginning or end of the dataset where the translated " + "values are not known, use missing values (default is to remove those " + "instances)";
    }

    /**
     * Gets whether missing values should be used rather than removing instances
     * where the translated value is not known (due to border effects).
     * 
     * @return true if so
     */
    public boolean getFillWithMissing() {

        return m_FillWithMissing;
    }

    /**
     * Sets whether missing values should be used rather than removing instances
     * where the translated value is not known (due to border effects).
     * 
     * @param newFillWithMissing true if so
     */
    public void setFillWithMissing(boolean newFillWithMissing) {

        m_FillWithMissing = newFillWithMissing;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String instanceRangeTipText() {
        return "The number of instances forward/backward to merge values between. " + "A negative number indicates taking values from a past instance.";
    }

    /**
     * Gets the number of instances forward to translate values between. A negative
     * number indicates taking values from a past instance.
     * 
     * @return Value of InstanceRange.
     */
    public int getInstanceRange() {

        return m_InstanceRange;
    }

    /**
     * Sets the number of instances forward to translate values between. A negative
     * number indicates taking values from a past instance.
     * 
     * @param newInstanceRange Value to assign to InstanceRange.
     */
    public void setInstanceRange(int newInstanceRange) {

        m_InstanceRange = newInstanceRange;
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String invertSelectionTipText() {
        return "Invert matching sense. ie calculate for all non-specified columns.";
    }

    /**
     * Get whether the supplied columns are to be removed or kept
     * 
     * @return true if the supplied columns will be kept
     */
    public boolean getInvertSelection() {

        return m_SelectedCols.getInvert();
    }

    /**
     * Set whether selected columns should be removed or kept. If true the selected
     * columns are kept and unselected columns are copied. If false selected columns
     * are copied and unselected columns are kept.
     * 
     * @param invert the new invert setting
     */
    public void setInvertSelection(boolean invert) {

        m_SelectedCols.setInvert(invert);
    }

    /**
     * Returns the tip text for this property
     * 
     * @return tip text for this property suitable for displaying in the
     *         explorer/experimenter gui
     */
    public String attributeIndicesTipText() {
        return "Specify range of attributes to act on." + " This is a comma separated list of attribute indices, with" + " \"first\" and \"last\" valid values. Specify an inclusive" + " range with \"-\". E.g: \"first-3,5,6-10,last\".";
    }

    /**
     * Get the current range selection
     * 
     * @return a string containing a comma separated list of ranges
     */
    public String getAttributeIndices() {

        return m_SelectedCols.getRanges();
    }

    /**
     * Set which attributes are to be copied (or kept if invert is true)
     * 
     * @param rangeList a string representing the list of attributes. Since the
     *                  string will typically come from a user, attributes are
     *                  indexed from 1. <br>
     *                  eg: first-3,5,6-last
     */
    public void setAttributeIndices(String rangeList) {

        m_SelectedCols.setRanges(rangeList);
    }

    /**
     * Set which attributes are to be copied (or kept if invert is true)
     * 
     * @param attributes an array containing indexes of attributes to select. Since
     *                   the array will typically come from a program, attributes
     *                   are indexed from 0.
     */
    public void setAttributeIndicesArray(int[] attributes) {

        setAttributeIndices(Range.indicesToRangeList(attributes));
    }

    /** Clears any instances from the history queue. */
    protected void resetHistory() {

        if (m_History == null) {
            m_History = new Queue();
        } else {
            m_History.removeAllElements();
        }
    }

    /**
     * Adds an instance to the history buffer. If enough instances are in the
     * buffer, a new instance may be output, with selected attribute values copied
     * from one to another.
     * 
     * @param instance the input instance
     * @return a new instance with translated values, or null if no output instance
     *         is produced
     */
    protected Instance historyInput(Instance instance) {

        m_History.push(instance);
        if (m_History.size() <= Math.abs(m_InstanceRange)) {
            if (getFillWithMissing() && (m_InstanceRange < 0)) {
                return mergeInstances(null, instance);
            } else {
                return null;
            }
        }
        if (m_InstanceRange < 0) {
            return mergeInstances((Instance) m_History.pop(), instance);
        } else {
            return mergeInstances(instance, (Instance) m_History.pop());
        }
    }

    /**
     * Creates a new instance the same as one instance (the "destination") but with
     * some attribute values copied from another instance (the "source")
     * 
     * @param source the source instance
     * @param dest   the destination instance
     * @return the new merged instance
     */
    protected abstract Instance mergeInstances(Instance source, Instance dest);

}
